A Neanderthal in the family: working with ancient DNA

Prof. Svante P��bo gave one of the plenary lectures at AAAS, describing his …

One of the highlights of the AAAS meeting in Chicago, other than the opportunity to hang out with some of my Ars colleagues in real life, was the plenary given by Prof. Svante P��bo, Director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig. Regular readers will remember our past coverage of Prof. P��bo's efforts to sequence the Neanderthalgenome, and his very well-attended plenary at AAAS served as an overview of the past couple of years' work from P��bo and his collaborators.

As you might imagine, getting viable DNA out of bones that are tens of thousands of years old is no mean feat. But being able to do so offers scientists the chance to learn a lot about the evolution of humans by comparing our genome with that of the Neanderthal (last common ancestor: 300,000-500,000 years ago) and the chimpanzee (last common ancestor: ~6 million years ago). Prof. P��bo spoke a little on some of the technical challenges involved in working with ancient DNA, and then went into some detail on some of the findings that have resulted.

Working with ancient DNA

Work with ancient DNA began with samples extracted from Egyptian mummies. Although well preserved macroscopically, most mummies have degraded to the point where histology or molecular biology is impossible. However, a few specimens were able to provide traces of DNA that gave researchers something to start honing their skills on. It became obvious that after these long timeframes, the DNA recovered was usually short (100 base pairs or less) and sometimes featured chemical modifications that needed to be accounted for in sequencing.

In 1997, the first DNA samples were recovered from H. neaderthalensis; in fact, these were obtained from the original fossil discovered in the Neander valley. At first, the decision was made to focus on the mitochondrial (mt)DNA. There's much more mtDNA in a cell than genomic DNA, since there are lots of mitochondria but only one nucleus, so getting enough to work with is easier.

Human mtDNA points to a population bottleneck and a single matrilinear origin (known as mitochondrial eve) that occurred over 100,000 years ago. If the assimilation theory regarding Neanderthals (that they interbred with humans) was correct, then sequencing the Neanderthal mtDNA might have placed the Neanderthal mtDNA within our own lineage. Unfortunately for proponents of this theory, the DNA sequences suggest the mitochondrial lineage of the Neanderthal specimen was much older, indicating we last shared a common ancestor with them around 600,000 years ago.

Controlling for contamination and damage, P��bo and his group were then able to start looking at specific genes of interest, as well as answering some significant questions. One of the biggest ones was "how far back do you have to go to get to our common ancestor?"

So the next step was to look at the genomic DNA. Although mitochondrial eve was relatively recent in our prehistory, some variations in the human genome date back to around 1 million years, so the assimilation theory could still be tested. Researchers are also interested in looking at genes we know have undergone recent evolutionary changes in humans, such as FOXP2, involved in language, and microcephalin, which is involved in brain size.

To get genomic DNA, P��bo and his team extracted DNA from more than 70 bones, obtained at 16 different sites, from El Sidron in Spain to Mezmaiskaya in Russia. These bones were analyzed for Neanderthal genetic markers, which showed that most of them contained no Neanderthal DNA. The best DNA was recovered from the Spanish site, the Neander valley specimen, remains from Vindija in Croatia, and Mezmaiskaya in Russia. These samples, along with technology improvements by 454 and Illumina (makers of DNA sequencing systems), have allowed P��bo to meet his goal of achieving 1x coverage of the Neanderthal genome by 2008.

Even that has been tricky though; only about four percent of the DNA recovered from the specimens is actually hominid DNA. The rest is microbial, but by designing restriction enzymes that chew up this microbial DNA but not hominid DNA, they have been able to boost their yields to around 20 percent.

The DNA is extracted under clean conditions in the lab, and then tagged with a short sequence that helps to control for contamination with modern human DNA; this gets them to the point where contaminant DNA is only around 0.5 percent. Work with the mtDNA sequence, which now has 800-fold coverage, taught P��bo that there was a quite common form of damage, where C misreads as T close to the 5' end, and G misreads as A close to the 3' end. This has to be factored in when reconstructing the entire genome from fragments of less than 100 base pairs.

Looking into the Neanderthal genome

Controlling for contamination and damage, P��bo and his group were then able to start looking at specific genes of interest, as well as answering some significant questions. One of the biggest ones was "how far back do you have to go to get to our common ancestor?"

As I mentioned earlier, there's quite a lot of divergence between human populations; representative French ethnic DNA differs from the reference human sequence by around eight percent, as does Han Chinese. Some African populations, such as the Mbute, differ by almost 11 percent. By multiplying these percentages by the time since the last common ancestor with chimpanzees (6.5 MYa) it is possible to come up with a rough date of divergence. The Neanderthal genome has around 12.8 percent variation, which places its divergence at around 830,000 years ago.

Looking at specific genes of interest seems to torpedo the assimilation theory, at least for now. Lactose tolerance has been a relatively recent evolution in Europeans (although it has also arisen several times since then). The Neanderthal genome seems to contain an ancestral version, suggesting that, like me, they would not have enjoyed a pint of Ben and Jerry's as much as my editor does.

FOXP2 has a pair of human-specific changes that are thought to be involved in our use of language; these were also seen in Neanderthals, so it's reasonable to assume that like us, they could communicate with each other effectively. Other genes, such as Tau and microcephalin that have recent human variants, also only showed up as the older, ancestral forms.

As P��bo put it, the data are fairly clear that there's no evidence for mixing between European and Neanderthal populations. However, the absence of evidence is not the evidence of absence, as they say, and his team is now looking at whether genes seen in early humans might have then been transferred to Neanderthals.

Great article! I'm a bit confused on one thing though. The Neanderthal's had a lactose tolerance gene but would not have liked ice cream? I don't get what you are saying there. Do they not have a good lactose tolerance gene?

Originally posted by skicow:Nice article -- thanks for the update on where we stand with Neanderthal mixing.

I personally am on the side that believes we Humans interbred with Neanderthals.

I also tend toward this idea.

I would think that most of the Neanderthals were killed by Homosapiens especially the male populations. The remaining female population were probably subsumed into the Homosapien population thru breeding...

Originally posted by mrjk:Great article! I'm a bit confused on one thing though. The Neanderthal's had a lactose tolerance gene but would not have liked ice cream? I don't get what you are saying there. Do they not have a good lactose tolerance gene?

What the article is saying is that the gene is related to lactose tolerance not that having the gene causes lactose tolerance. As Neanderthals had an ancient version of the gene, it likely caused lactose intolerance.

They aren't that different in appearance, especially considering home sapiens was not any cleaner nor dressed any better at the time.

Genetic intermingling often happens in less than ideal conditions. War zones, for example. The victims of rape don't have to be young, pretty or desirable at all, they simply need to have the misfortune to be in the wrong place at the wrong time. And some men will have sex with anything, vaguely human or not. (And some women have equally... alternative... tastes.)

Whether the offspring would have been viable is hopefully one question this study will begin to address.

Originally posted by KrancHammer:They certainly aren't any more different in appearance than say, a Spanish European male and an Aztec or Mayan female.

Patently untrue. Very different face and skull shapes. Much more different than any variation among homo sapiens. And the body shape and posture was different. Neanderthal were notably stockier. Enough difference in body design that you would have been able to tell the difference between neanderthals and humans from a distance just by seeing them walk or run.

quote:

originally posted by NicoleC:The victims of rape don't have to be young, pretty or desirable at all, they simply need to have the misfortune to be in the wrong place at the wrong time.

Rape is one thing. The comment I was responding to was about incorporating female neanderthals into the human tribal group -- i.e. taking them as wives/slaves/concubines.

The question is not whether a human and a neanderthal ever had sex. The question is whether there would have been any significant level of interbreeding, were breeding even possible.

Finally, at this point in our genetic understanding there is no way to figure out whether breeding would be possible just by looking at DNA sequences. There's just too many variables.

Well I wouldn't expect to find too much maternal DNA to be quite honest. I would think a female neanderthal wouldn't rank very highly among human males. Really, would you consider it?

The neanderthal females shared many male qualities we find undesirable. Likewise, I would think the neanderthal women might find the human males too feminine compared to the neanderthal males.

I would guess it would be highly more likely for neanderthal males to mate with human females. They offer fewer male characteristics, and separation of gender is often a source of attraction. The taller, more muscular build of a neanderthal might not have been all that repulsive for human females either..

Maybe neanderthals are extinct because neanderthal women weren't nearly as appealing as human women. It would be a quick end to a species if all the males stopped mating with the females of the species.

I personally am on the side that believes we Humans interbred with Neanderthals.

Believe what you want. I fear science must go by evidence.

quote:

Great article! I'm a bit confused on one thing though. The Neanderthal's had a lactose tolerance gene but would not have liked ice cream? I don't get what you are saying there.

The Ars article seems rather confused at this point. Maybe the wording is unfortunate and we're both misreading it in some way. Or maybe the author got distracted by his own joke about ice cream.

Really, one would not expect Neanderthaler *adults* to be tolerant of lactose ("milk sugar"). Such tolerance seems to have arisen with the advent of farming and consequent exploitation of milk as food. And it's milk, or milk derivatives, in an unfermented state that can be hard for adults to digest. (Yoghurt is OK.)

One can soon verify that things are as one would expect by googling:

neanderthal "lactose intolerance"

quote:

Other insights gained from a preliminary analysis of the Neanderthal genome are that the species could not drink milk as adults – they have the same lactose intolerance seen in the majority of modern humans ...

As Pääbo put it, the data are fairly clear that there's no evidence for mixing between European and Neanderthal populations. However, the absence of evidence is not the evidence of absence, as they say ...

Do "they"? This seems a rather broader claim that the obvious statement that in Science findings are subject to revision. I suppose on that basis "they" can make just about any claim that suits "them".

Originally posted by mrjk:Great article! I'm a bit confused on one thing though. The Neanderthal's had a lactose tolerance gene but would not have liked ice cream? I don't get what you are saying there. Do they not have a good lactose tolerance gene?

What the article is saying is that the gene is related to lactose tolerance not that having the gene causes lactose tolerance. As Neanderthals had an ancient version of the gene, it likely caused lactose intolerance.

Right. Some humans have a recent mutation in the gene that allows adults to digest cows milk - humans descended from ancestors who weren't in this population with the "i can drink cow juice" mutation can't handle milk, and this older version of the gene is the one shared with the neanderthals.

Originally posted by skicow:I personally am on the side that believes we Humans interbred with Neanderthals.

I also tend toward this idea.

I must admit, I used to as well, but all the evidence is pointing in the opposite direction. What makes you two still believe otherwise?

If the Neanderthal DNA they've collected has come from a wide range all across Europe, and it contains no human DNA, why do you still think they interbred? It may have happened on occassion, but there appears no chance the Neanderthals were assimilated or absorbed into our ancestors populations.

This (incredibly interesting) research has made me change my mind. I'm now thinking it either looks like we wiped out/out competed the Neanderthals, or there was some other natural disaster (e.g. disease or climate change) that demolished their populations.

"NicoleCThey aren't that different in appearance, especially considering home sapiens was not any cleaner nor dressed any better at the time.

Genetic intermingling often happens in less than ideal conditions. War zones, for example. The victims of rape don't have to be young, pretty or desirable at all, they simply need to have the misfortune to be in the wrong place at the wrong time. And some men will have sex with anything, vaguely human or not. (And some women have equally... alternative... tastes.)

Whether the offspring would have been viable is hopefully one question this study will begin to address."

Dead on NicoleC.

Remember the guy they caught having sex with a chicken? The question is whether offspring would be fertile or "mule". As for physical differences compare our own variation - say between Dr. Ruth and Patrick Ewing as two who look little alike and have enormous difference in size - apologies to those unfamiliar with US cultural figures.

you mention both species have the FOXP2 genome having to do with large brain size and/or communication ability. i recall in another article that this was exactly the gene that was theorized to have transfered from h. neanderthal to h. sapiens.

i'm not sure i entirely understand the mitochondrial eve connection... could it not be that the h. neanderthal population and the h. sapiens population diverged 6k years ago, then interbred again later? does it logically follow that if we are descended from a h. sapiens and h. neanderthal hybrid, that we would share a mitochondrial eve ancestor with the h. neanderthal stock?

i think i need to read the original material to see if i can grok it. it took me a while to grasp mitochondrial eve and y-chromosome adam in the first place.

i think homo neanderthals and homo sapiens look rather similar. some of the more modern reconstructions using state of the art forensic techniques actually look rather attractive to me, but then again i like butch women. the older, less accurate reconstructions are the ones that look so much like grunting "cave men" of lore.

the reconstructed images of neanderthals look more like western europeans more than does, say, the typical mayan to me. i'd say they look rather french if i had to pick a race. on the other hand cro-magnon man was probably far more homogenous looking than we are today, having recently survived a population bottleneck and being a wave of o, and neanderthals may have looked very strange to them indeed.

on the other hand if there is no evidence of genetic crossover then that proves that the two species were not genetically compatible, and therefore truly different species. because we can guarantee that some humans tried to mate with them.

i think homo neanderthals and homo sapiens look rather similar. some of the more modern reconstructions using state of the art forensic techniques actually look rather attractive to me, but then again i like butch women. the older, less accurate reconstructions are the ones that look so much like grunting "cave men" of lore.

the reconstructed images of neanderthals look more like western europeans more than does, say, the typical mayan to me. i'd say they look rather french if i had to pick a race. on the other hand cro-magnon man was probably far more homogenous looking than we are today, having recently survived a population bottleneck and being a wave of o, and neanderthals may have looked very strange to them indeed.

on the other hand if there is no evidence of genetic crossover then that proves that the two species were not genetically compatible, and therefore truly different species. because we can guarantee that some humans tried to mate with them.